1
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Heid LF, Agerschou ED, Orr AA, Kupreichyk T, Schneider W, Wördehoff MM, Schwarten M, Willbold D, Tamamis P, Stoldt M, Hoyer W. Sequence-based identification of amyloidogenic β-hairpins reveals a prostatic acid phosphatase fragment promoting semen amyloid formation. Comput Struct Biotechnol J 2024; 23:417-430. [PMID: 38223341 PMCID: PMC10787225 DOI: 10.1016/j.csbj.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
β-Structure-rich amyloid fibrils are hallmarks of several diseases, including Alzheimer's (AD), Parkinson's (PD), and type 2 diabetes (T2D). While amyloid fibrils typically consist of parallel β-sheets, the anti-parallel β-hairpin is a structural motif accessible to amyloidogenic proteins in their monomeric and oligomeric states. Here, to investigate implications of β-hairpins in amyloid formation, potential β-hairpin-forming amyloidogenic segments in the human proteome were predicted based on sequence similarity with β-hairpins previously observed in Aβ, α-synuclein, and islet amyloid polypeptide, amyloidogenic proteins associated with AD, PD, and T2D, respectively. These three β-hairpins, established upon binding to the engineered binding protein β-wrapin AS10, are characterized by proximity of two sequence segments rich in hydrophobic and aromatic amino acids, with high β-aggregation scores according to the TANGO algorithm. Using these criteria, 2505 potential β-hairpin-forming amyloidogenic segments in 2098 human proteins were identified. Characterization of a test set of eight protein segments showed that seven assembled into Thioflavin T-positive aggregates and four formed β-hairpins in complex with AS10 according to NMR. One of those is a segment of prostatic acid phosphatase (PAP) comprising amino acids 185-208. PAP is naturally cleaved into fragments, including PAP(248-286) which forms functional amyloid in semen. We find that PAP(185-208) strongly decreases the protein concentrations required for fibril formation of PAP(248-286) and of another semen amyloid peptide, SEM1(86-107), indicating that it promotes nucleation of semen amyloids. In conclusion, β-hairpin-forming amyloidogenic protein segments could be identified in the human proteome with potential roles in functional or disease-related amyloid formation.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Asuka A. Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Michael M. Wördehoff
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Melanie Schwarten
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843-3033, United States
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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2
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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3
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Galkin M, Priss A, Kyriukha Y, Shvadchak V. Navigating α-Synuclein Aggregation Inhibition: Methods, Mechanisms, and Molecular Targets. CHEM REC 2024; 24:e202300282. [PMID: 37919046 DOI: 10.1002/tcr.202300282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/08/2023] [Indexed: 11/04/2023]
Abstract
Parkinson's disease is a yet incurable, age-related neurodegenerative disorder characterized by the aggregation of small neuronal protein α-synuclein into amyloid fibrils. Inhibition of this process is a prospective strategy for developing a disease-modifying treatment. We overview here small molecule, peptide, and protein inhibitors of α-synuclein fibrillization reported to date. Special attention was paid to the specificity of inhibitors and critical analysis of their action mechanisms. Namely, the importance of oxidation of polyphenols and cross-linking of α-synuclein into inhibitory dimers was highlighted. We also compared strategies of targeting monomeric, oligomeric, and fibrillar α-synuclein species, thoroughly discussed the strong and weak sides of different approaches to testing the inhibitors.
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Affiliation(s)
- Maksym Galkin
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anastasiia Priss
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yevhenii Kyriukha
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States
| | - Volodymyr Shvadchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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4
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Schulz CM, Pfitzer A, Hoyer W. Fibril core regions in engineered α-synuclein dimer are crucial for blocking of fibril elongation. BBA ADVANCES 2023; 4:100110. [PMID: 38053641 PMCID: PMC10694066 DOI: 10.1016/j.bbadva.2023.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/20/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
Synucleinopathies like Parkinson's disease are neurodegenerative diseases which are associated with the deposition of fibrillar aggregates of the endogenous protein α-synuclein (α-syn). The inhibition of the elongation of α-syn fibrils is of great scientific interest and an option in the design of therapeutic strategies. Previously, we developed a disulfide-containing mutant of α-syn, called CC48, which inhibits fibril elongation by blocking of fibril ends. Surprisingly, wildtype (WT) α-syn molecules supported the blocked state, and a fusion of CC48 with WT α-syn, denoted WT-CC48, exhibited increased inhibitory potential. Here, we studied which regions of WT-CC48 are responsible for the strong inhibitory effect. To this end, we investigated a set of truncated versions of WT-CC48 by kinetic elongation assays, density gradient centrifugation, and atomic force microscopy. We show that in both the WT and the CC48 part of the fusion construct the hairpin region (residue 32-60) and NAC region (61-95), but not N- and C-terminal regions, are required for strong inhibition of fibril elongation. The required regions correspond to the segments forming the β-sheet core of α-syn fibrils. As α-syn fibrils typically consist of two protofilaments, the dimeric construct WT-CC48 provides the critical regions sufficient to cover the full β-sheetcore interface exposed at the fibril end, which can explain its high inhibitory efficiency. We suggest a mechanistic model of CC48-mediated inhibition of fibril elongation in which CC48 and WT α-syn cooperatively form an oligomer-like cap at the amyloid fibril end.
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Affiliation(s)
- Celina M. Schulz
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anne Pfitzer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
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5
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Heid LF, Kupreichyk T, Schützmann MP, Schneider W, Stoldt M, Hoyer W. Nucleation of α-Synuclein Amyloid Fibrils Induced by Cross-Interaction with β-Hairpin Peptides Derived from Immunoglobulin Light Chains. Int J Mol Sci 2023; 24:16132. [PMID: 38003322 PMCID: PMC10671648 DOI: 10.3390/ijms242216132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Heterologous interactions between different amyloid-forming proteins, also called cross-interactions, may have a critical impact on disease-related amyloid formation. β-hairpin conformers of amyloid-forming proteins have been shown to affect homologous interactions in the amyloid self-assembly process. Here, we applied two β-hairpin-forming peptides derived from immunoglobulin light chains as models to test how heterologous β-hairpins modulate the fibril formation of Parkinson's disease-associated protein α-synuclein (αSyn). The peptides SMAhp and LENhp comprise β-strands C and C' of the κ4 antibodies SMA and LEN, which are associated with light chain amyloidosis and multiple myeloma, respectively. SMAhp and LENhp bind with high affinity to the β-hairpin-binding protein β-wrapin AS10 according to isothermal titration calorimetry and NMR spectroscopy. The addition of SMAhp and LENhp affects the kinetics of αSyn aggregation monitored by Thioflavin T (ThT) fluorescence, with the effect depending on assay conditions, salt concentration, and the applied β-hairpin peptide. In the absence of agitation, substoichiometric concentrations of the hairpin peptides strongly reduce the lag time of αSyn aggregation, suggesting that they support the nucleation of αSyn amyloid fibrils. The effect is also observed for the aggregation of αSyn fragments lacking the N-terminus or the C-terminus, indicating that the promotion of nucleation involves the interaction of hairpin peptides with the hydrophobic non-amyloid-β component (NAC) region.
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Affiliation(s)
- Laetitia F. Heid
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Marie P. Schützmann
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Walfried Schneider
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
| | - Matthias Stoldt
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, 40204 Düsseldorf, Germany
- Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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Galkin M, Topcheva O, Priss A, Borisova T, Shvadchak VV. Dopamine-Induced Oligomers of α-Synuclein Inhibit Amyloid Fibril Growth and Show No Toxicity. ACS Chem Neurosci 2023. [PMID: 37162160 DOI: 10.1021/acschemneuro.2c00815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Parkinson's disease is characterized by the selective death of dopaminergic neurons in the midbrain and accumulation of amyloid fibrils composed of α-synuclein (αSyn). Current treatment involves approaches that compensate the death of dopaminergic neurons by increasing the dopamine levels in remaining cells. However, dopamine can interact with αSyn and produce oligomeric species which were reported to be toxic in many models. We studied formation of dopamine-induced αSyn oligomers and their effect on the αSyn aggregation. Using the Thioflavin T kinetic assay, we have shown that small oligomers efficiently inhibit αSyn fibrillization by binding to fibril ends and blocking the elongation. Moreover, all the fractions of oligomer species proved to be nontoxic in the differentiated SH-SY5Y cell model and showed negligible neurotoxicity on isolated rat synaptosomes. The observed inhibition is an important insight in understanding of dopamine-enhancing therapy on Parkinson's disease progression and explains the absence of pathology enhancement.
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Affiliation(s)
- Maksym Galkin
- Laboratory of Chemical Biology, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Oleksandra Topcheva
- Laboratory of Chemical Biology, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Anastasiia Priss
- Laboratory of Chemical Biology, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Tatiana Borisova
- Department of Neurochemistry, Palladin Institute of Biochemistry, National Academy of Sciences of Ukraine, 9 Leontovycha Street, Kyiv 01054, Ukraine
| | - Volodymyr V Shvadchak
- Laboratory of Chemical Biology, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, 57 Shevchenko Str., Ivano-Frankivsk 76018, Ukraine
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7
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Bopardikar M, Koti Ainavarapu SR, Hosur RV. Pyrogallol, Corilagin and Chebulagic acid target the "fuzzy coat" of alpha-synuclein to inhibit the fibrillization of the protein. RSC Adv 2022; 12:35770-35777. [PMID: 36545068 PMCID: PMC9749937 DOI: 10.1039/d2ra04358k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/13/2022] [Indexed: 12/15/2022] Open
Abstract
The accumulation of the intrinsically disordered protein alpha-synuclein (αSyn) in the form of insoluble fibrillar aggregates in the central nervous system is linked to a variety of neurodegenerative disorders such as Parkinson's disease, Lewy body dementia, and multiple system atrophy. Here we show that Pyrogallol, Corilagin and Chebulagic acid, compounds containing a different number of catechol rings, are independently capable of delaying and reducing the extent of αSyn fibrillization. The efficiency of inhibition was found to correlate with the number of catechol rings. Further, our NMR studies reveal that these compounds interact with the N-terminal region of αSyn which is unstructured even in the fibrillar form of the protein and is known as the "fuzzy coat" of fibrils. Thus, Corilagin and Chebulagic acid target the fuzzy coat of αSyn and not the amyloid core which is a common target for the inhibition of protein fibrillization. Our results indicate that the N-terminus also plays a key role in the fibrillization of αSyn.
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Affiliation(s)
- Mandar Bopardikar
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental ResearchHomi Bhabha Road, ColabaMumbai 400005India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina CampusSantacruzMumbai 400098India
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8
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:ijms232113428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9600503916
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9
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Hu J, Zhao Y, Li Y. Rationally designed amyloid inhibitors based on amyloid-related structural studies. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Braczynski AK, Sevenich M, Gering I, Kupreichyk T, Agerschou ED, Kronimus Y, Habib P, Stoldt M, Willbold D, Schulz JB, Bach JP, Falkenburger BH, Hoyer W. Alpha-Synuclein-Specific Naturally Occurring Antibodies Inhibit Aggregation In Vitro and In Vivo. Biomolecules 2022; 12:biom12030469. [PMID: 35327661 PMCID: PMC8946620 DOI: 10.3390/biom12030469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is associated with motor and non-motor symptoms and characterized by aggregates of alpha-synuclein (αSyn). Naturally occurring antibodies (nAbs) are part of the innate immune system, produced without prior contact to their specific antigen, and polyreactive. The abundance of nAbs against αSyn is altered in patients with PD. In this work, we biophysically characterized nAbs against αSyn (nAbs-αSyn) and determined their biological effects. nAbs-αSyn were isolated from commercial intravenous immunoglobulins using column affinity purification. Biophysical properties were characterized using a battery of established in vitro assays. Biological effects were characterized in HEK293T cells transiently transfected with fluorescently tagged αSyn. Specific binding of nAbs-αSyn to monomeric αSyn was demonstrated by Dot blot, ELISA, and Surface Plasmon Resonance. nAbs-αSyn did not affect viability of HEK293T cells as reported by Cell Titer Blue and LDH Assays. nAbs-αSyn inhibited fibrillation of αSyn reported by the Thioflavin T aggregation assay. Altered fibril formation was confirmed with atomic force microscopy. In cells transfected with EGFP-tagged αSyn we observed reduced formation of aggresomes, perinuclear accumulations of αSyn aggregates. The results demonstrate that serum of healthy individuals contains nAbs that specifically bind αSyn and inhibit aggregation of αSyn in vitro. The addition of nAbs-αSyn to cultured cells affects intracellular αSyn aggregates. These findings help understanding the role of the innate immune systems for the pathogenesis of PD and suggest that systemic αSyn binding agents could potentially affect neuronal αSyn pathology.
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Affiliation(s)
- Anne K. Braczynski
- Department of Neurology, RWTH University Hospital, 52074 Aachen, Germany; (A.K.B.); (P.H.); (J.B.S.); (J.-P.B.)
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
| | - Marc Sevenich
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
- Priavoid GmbH, 40225 Düsseldorf, Germany
| | - Ian Gering
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
| | - Tatsiana Kupreichyk
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
| | - Emil D. Agerschou
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
| | - Yannick Kronimus
- Department of Geriatric Medicine, University Hospital Essen, University Duisburg-Essen, 47057 Duisburg, Germany;
| | - Pardes Habib
- Department of Neurology, RWTH University Hospital, 52074 Aachen, Germany; (A.K.B.); (P.H.); (J.B.S.); (J.-P.B.)
- Institute of Biochemistry and Molecular Immunology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
| | - Jörg B. Schulz
- Department of Neurology, RWTH University Hospital, 52074 Aachen, Germany; (A.K.B.); (P.H.); (J.B.S.); (J.-P.B.)
- JARA-Institute Molecular Neuroscience and Neuroimaging, Jülich Aachen Research Alliance, FZ Jülich and RWTH University, 52428 Jülich, Germany
| | - Jan-Philipp Bach
- Department of Neurology, RWTH University Hospital, 52074 Aachen, Germany; (A.K.B.); (P.H.); (J.B.S.); (J.-P.B.)
| | - Björn H. Falkenburger
- Department of Neurology, RWTH University Hospital, 52074 Aachen, Germany; (A.K.B.); (P.H.); (J.B.S.); (J.-P.B.)
- Department of Neurology, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- Correspondence: (B.H.F.); (W.H.)
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany; (T.K.); (E.D.A.); (M.S.); (D.W.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (M.S.); (I.G.)
- Correspondence: (B.H.F.); (W.H.)
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11
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Galkin M, Priss A, Topcheva O, Yushchenko DA, Shvadchak VV. FRET-based assay for intracellular evaluation of α-synuclein aggregation inhibitors. J Neurochem 2021; 159:901-912. [PMID: 34687236 DOI: 10.1111/jnc.15528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 01/01/2023]
Abstract
Aggregation of small neuronal protein α-synuclein (αSyn) in amyloid fibrils is considered to be one of the main causes of Parkinson's disease. Inhibition of this aggregation is a promising approach for disease treatment. Dozens of compounds able to inhibit αSyn fibrillization in solution were developed during the last decade. However, the applicability of most of them in the cellular environment was not established because of the absence of a suitable cell-based assay. In this work, we developed an assay for testing αSyn aggregation inhibitors in cells that is based on fluorescence resonance energy transfer (FRET) between labeled αSyn molecules in fibrils. The assay directly reports the amount of fibrillized αSyn and is more reliable than the assays based on cell viability. Moreover, we showed that cell viability decline does not always correlate with the amount of misfolded αSyn. The developed FRET-based assay does not interfere with the aggregation process and is suitable for high-throughput testing of αSyn aggregation inhibitors. Its application can sort out non-specific inhibitors and thus significantly facilitate the development of drugs for Parkinson`s disease.
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Affiliation(s)
- Maksym Galkin
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Faculty of Science, Department of Biochemistry, Charles University, Prague, Czech Republic
| | - Anastasiia Priss
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Faculty of Science, Department of Biochemistry, Charles University, Prague, Czech Republic
| | - Oleksandra Topcheva
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dmytro A Yushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Volodymyr V Shvadchak
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.,Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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12
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Priss A, Afitska K, Galkin M, Yushchenko DA, Shvadchak VV. Rationally Designed Protein-Based Inhibitor of α-Synuclein Fibrillization in Cells. J Med Chem 2021; 64:6827-6837. [PMID: 33970620 DOI: 10.1021/acs.jmedchem.1c00086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Misfolding of the neuronal protein α-synuclein (αSyn) into amyloid fibrils is involved in the development of Parkinson's disease (PD), and inhibition of this process is considered to be a promising therapeutic approach. In this work, we engineered protein inhibitors that bind to fibrils with higher affinity than the monomeric αSyn. They were developed based on the recent structural data of the αSyn fibrils and were shown to prevent fibril elongation upon binding to fibril ends. These inhibitors are highly selective to the misfolded αSyn, nontoxic, and active in cytosol in small concentrations. The best-performing inhibitor shows IC50 ∼10 nM in a cell-based assay, which corresponds to the ∼1:60 molar ratio to αSyn. It can suppress the formation of αSyn aggregates in cells that can be potentially used to slow down the spreading of the pathological aggregates from cell to cell during the course of the PD.
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Affiliation(s)
- Anastasiia Priss
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, Prague 12843, Czech Republic
| | - Kseniia Afitska
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, Prague 16610, Czech Republic
| | - Maksym Galkin
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Albertov 6, Prague 12843, Czech Republic
| | - Dmytro A Yushchenko
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, Prague 16610, Czech Republic.,Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, Bergisch Gladbach D-51429, Germany
| | - Volodymyr V Shvadchak
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, Prague 16610, Czech Republic
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13
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Agerschou ED, Schützmann MP, Reppert N, Wördehoff MM, Shaykhalishahi H, Buell AK, Hoyer W. β-Turn exchanges in the α-synuclein segment 44-TKEG-47 reveal high sequence fidelity requirements of amyloid fibril elongation. Biophys Chem 2021; 269:106519. [PMID: 33333378 DOI: 10.1016/j.bpc.2020.106519] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 11/30/2020] [Indexed: 11/28/2022]
Abstract
The folding of turns and β-hairpins has been implicated in amyloid formation, with diverse potential consequences such as promotion or inhibition of fibril nucleation, fibril elongation, or off-pathway oligomer formation. In the Parkinson's disease-associated protein α-synuclein (αS), a β-hairpin comprised of residues 36-56 was detected in complex with an engineered binding protein, with a turn formed by the αS sequence segment 44-TKEG-47. Molecular dynamics simulations revealed extensive populations of transient β-hairpin conformations in this region in free, monomeric αS. Here, we investigated potential effects of turn formation on αS fibril formation by studying the aggregation kinetics of an extensive set of αS variants with between two and four amino acid exchanges in the 44-TKEG-47 segment. The exchanges were chosen to specifically promote formation of β1-, β1'-, or β2'-turns. All variants assembled into amyloid fibrils, with increased β1'- or β2'-turn propensity associated with faster aggregation and increased β1-turn propensity with slower aggregation compared to wild-type (WT) αS. Atomic force microscopy demonstrated that β-turn exchanges altered fibril morphology. In cross-elongation experiments, the turn variants showed a low ability to elongate WT fibril seeds, and, vice versa, WT monomer did not efficiently elongate turn variant fibril seeds. This demonstrates that sequence identity in the turn region is crucial for efficient αS fibril elongation. Elongation experiments of WT fibril seeds in the presence of both WT and turn variant monomers suggest that the turn variants can bind and block WT fibril ends to different degrees, but cannot efficiently convert into the WT fibril structure. Our results indicate that modifications in the 44-TKEG-47 segment strongly affect amyloid assembly by driving αS into alternative fibril morphologies, whose elongation requires high sequence fidelity.
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Affiliation(s)
- Emil Dandanell Agerschou
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Marie P Schützmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Nikolas Reppert
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Michael M Wördehoff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Hamed Shaykhalishahi
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany
| | - Alexander K Buell
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40204 Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany.
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